Hello, all, It is quite common to encounter protein structures in PDB which consist of only the catalytic domain (versus the structure of the entire protein). One such example is: http://www.pdb.org/pdb/explore.do?structureId=1H1W
My questions: 1) Is it a good idea to use such catalytic domain structures for MD simulation? Or should I only use complete protein structures for MD? 2) Is there a way to constraint the atoms using Gromacs during MD at the points where the catalytic domain is 'chopped' from the rest of the protein? 2) If I want to use Gromacs to conduct a MD of 0.1ps at 300K, do I need to constraint any atoms at the 'edges' during the MD run? Thank you. Regards, wk yeo _________________________________________________________________ Manage multiple email accounts with Windows Live Mail effortlessly. http://www.get.live.com/wl/all _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
